X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fschemes%2FTCoffeeColourScheme.java;h=2be51c2b94a6f38e77960b912a3c247e1d047a68;hb=23e1ca45f5adac64d191f1e3e7d4d64ae52eaa03;hp=6eb48c24f0f5420fe300f112f69c26c1dfad4325;hpb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;p=jalview.git
diff --git a/src/jalview/schemes/TCoffeeColourScheme.java b/src/jalview/schemes/TCoffeeColourScheme.java
index 6eb48c2..2be51c2 100644
--- a/src/jalview/schemes/TCoffeeColourScheme.java
+++ b/src/jalview/schemes/TCoffeeColourScheme.java
@@ -1,24 +1,25 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
-import jalview.analysis.SequenceIdMatcher;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
@@ -31,7 +32,6 @@ import java.awt.Color;
import java.util.ArrayList;
import java.util.IdentityHashMap;
import java.util.Map;
-import java.util.TreeMap;
/**
* Defines the color score for T-Coffee MSA
@@ -45,8 +45,7 @@ import java.util.TreeMap;
public class TCoffeeColourScheme extends ResidueColourScheme
{
- static final Color[] colors =
- { new Color(102, 102, 255), // #6666FF
+ static final Color[] colors = { new Color(102, 102, 255), // #6666FF
new Color(0, 255, 0), // #00FF00
new Color(102, 255, 0), // #66FF00
new Color(204, 255, 0), // #CCFF00
@@ -85,8 +84,14 @@ public class TCoffeeColourScheme extends ResidueColourScheme
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
seqMap = new IdentityHashMap();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ : alignment.getContext();
+ if (alcontext == null)
+ {
+ return;
+ }
int w = 0;
- for (AlignmentAnnotation al : alignment
+ for (AlignmentAnnotation al : alcontext
.findAnnotation(TCoffeeScoreFile.TCOFFEE_SCORE))
{
if (al.sequenceRef != null && !al.belowAlignment)
@@ -129,4 +134,11 @@ public class TCoffeeColourScheme extends ResidueColourScheme
}
return cols[j];
}
+
+ @Override
+ public ColourSchemeI applyTo(AnnotatedCollectionI sg,
+ Map hiddenRepSequences)
+ {
+ return new TCoffeeColourScheme(sg);
+ }
}